I want to hook up a nano HPLC to a Thermo Q-Extactive for proteomics and some small protein complex analysis. I was all set to go with the new Thermo EASY nLC 1000. The sales rep from the company started out with Dionex and of course pointed out the versatility of the Dionex RSLC system and the lower price. For the immediate future, I will only be doing proteins but maybe small metabolites might also be a possibility. I went to see somebody else's system and the main complaint that the Dionex system wasn't fully integrated with the Thermo software. It would crash and also the system kept giving an error message for leaks but they couldn't find them. They mass spec, HPLC and computer would have to be rebooted to get rid of the error. Any opinions or advise on which system?

I have used both the Easy nLC 1000 and the Easy nLC II and have had good experiences overall. The easy nLC II might be a good option if you plan to work at lower pressures, it is a bit cheaper as it only goes up to 300bar, but the rest of the system appears to be very similar to the easy nLC 1000.

The primary downside to the Easy nLC 1000 in my opinion is the nano-viper fittings. The system is set up to use nano-viper fittings, which means you either have to purchase columns with the fittings already attached (expensive, and you have limited options of what stationary phases and lengths you can use) or you have to re-plumb the HPLC after install to use different fittings. We like packing our own columns and are frugal so we re-plumbed our HPLC with with some upchurch/Idex fittings and typically operate our system around 500bar, much higher and the fittings we are using have a tendency to pop open. I might be mistaken, but I think the Dionex might also use the nano-viper fittings by default.

I agree the integration of the Easy nLC software into the Thermo Xcalibur software is nice and very stable. It also comes with additional software that records pressure traces and flow traces for every run, so if you have a problem at some point you can look back and see what normal run looks like very easily. I have never used a dionex personally, but a colleague of mine with a Dionex has complained about the pain of using the software to set up methods for that HPLC.

Hi, we've been using Dionex RSLC nano with Q-Exactive for several months now and didn't have any problems in interface with XCalibur. The LC performance is quite stable (much better than with Eksigent systems we have), another advantage is that you can go up to 1,000 bar but you must use nano-Viper fittings. I didn't have any experience with EASY-nLC systems.

I will put it this way: you can buy a Ferrari (Dionex) or you can buy a decent VW (EasyLC 1000).

If you need the car to run races (do advanced LC setups etc), buy a Ferrari. If you just want to drive from work to home, buy the VW.

I have a nano3000 here and it is a robust system, RT reproducibility is amazing, had almost 0 down time in 1 year. Down side is Injection setup which I think is nightmarish if you want to do non-trap/aired trap setups (in our experience at least), and to be fair Chromaleon interface is equally bad.

Thanks for your input. We decided to go with the Easy nLC1000 for proteomics. We are going to have users with a variety of skill levels and decided that the Dionex system offered more than what we would use the system for. We are going to continue the other LC system for experiments that don't require nano flows.